@Chaos_Knight The MC has exactly zero poker face. Let's hope he will never need to negotiate with anyone again.
@GrimGriefer Actually the chapters only talked about duties and tariffs, which means something collected at the gates when stuff moves in and/or out of the city. It says nothing about taxes. He could still collect some of those. Although it would certainly make sense to mention such a thing now, not only afterwards. He also can't treat later merchants any different because they wouldn't be able to compete with these two otherwise. He's not primarily interested in money, but in fact it's suspicious if he doesn't collect it, plus when more and more people move in, he will need to also spend money to keep the town running.
For such a noob MC with no poker face, he was pretty unlucky to get so hard-boiled merchants as the first ones to negotiate with. Obviously the merchants would be greedy and try to get massive benefits on top of the already huge opportunity they were immediately offered. That's what being a true merchant is. However, if he had kicked these two out to try again with other merchants, these two would have definitely caused him problems, maybe even to the point of turning the town into a regular dungeon by having adventurers loot it. In the end the merchants wouldn't care even if they knew the place is in fact a monster dungeon in a peaceful disguise, they only want to make money. All that talk about suspicious was just talk to pressure the gullible MC. But if they can't make profit, things are different.